Code

Adding per-base inference#9

Code

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matsen merged 53 commits intomainmatsengrp/netam:mainfrom 3-per-basematsengrp/netam:3-per-baseCopy head branch name to clipboardFeb 14, 2024

+567-136

Commits

Commits on Jan 31, 2024

• enter rsmodels

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  243d327

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• Add mutation and base indicator creation function

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• Add new base index vectors to SHMoofDataset

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• new base idx indicator

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• can train rsmodel now

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• make format

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• Remove cnn_med_orig

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  e2c18d0

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• adding rscnn to experiment

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• adding profiling script

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• yes to wt_base_multiplier and no to central_base_mapping

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• oop continuing prev commit

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  eee5647

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• cleanup and moving around

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• format

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• adding loss weights

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Commits on Feb 1, 2024

• Add JoinedRSCNNModel and IndepRSCNNModel

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• adding wt_base_multiplier to other models

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• returning multiple losses

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• partway through recording multiple losses

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• Recording separate losses

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• wt_base_modifier

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• make format

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Commits on Feb 2, 2024

• returning logits

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• being able to set loss weights

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• more complex loss reduction

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• moving out load_shmoof_dataframes

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Commits on Feb 3, 2024

• excluding Ns from being considered as mutations

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• RSFivemer

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• format

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  902b2d0

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• bring name back

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• mask in kmer rates

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• joined and hybrid models

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Commits on Feb 5, 2024

• RSSHMoof

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• make format

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Commits on Feb 7, 2024

• things seem ready to train dnsms with netam-shm!

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• refactoring framework for generality

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• Add informative_site_count function

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• make format

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Commits on Feb 9, 2024

• Remove unnecessary comment in FivemerModel constructor

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• appropriate trimming of long sequences

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• better names

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Commits on Feb 12, 2024

• loss weight of 0.01

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• cleanup

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• docstrings

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Commits on Feb 13, 2024

• commit before moving to directly using log site rates

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• using site rate weights directly

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• comment

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• better name

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• comment

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• making rate masking consistent across models

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• comment

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Commits on Feb 14, 2024

• csv.gz now the format for DNSM; fixing tests

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• adding data dir

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• more _ignore dir making

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